Correcting for sequence biases in present/absent calls

The probe sequence of short oligonucleotides in Affymetrix microarray experiments can have a significant influence on present/absent calls of probesets with absent target transcripts. Probesets enriched for central Ts and depleted of central As in the perfect-match probes tend to be falsely classifi...

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Detalles Bibliográficos
Autores principales: Schuster, Eugene F, Blanc, Eric, Partridge, Linda, Thornton, Janet M
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2007
Materias:
Method
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2394774/
https://www.ncbi.nlm.nih.gov/pubmed/17594492
http://dx.doi.org/10.1186/gb-2007-8-6-r125
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author Schuster, Eugene F
Blanc, Eric
Partridge, Linda
Thornton, Janet M
author_facet Schuster, Eugene F
Blanc, Eric
Partridge, Linda
Thornton, Janet M
author_sort Schuster, Eugene F
collection PubMed
description The probe sequence of short oligonucleotides in Affymetrix microarray experiments can have a significant influence on present/absent calls of probesets with absent target transcripts. Probesets enriched for central Ts and depleted of central As in the perfect-match probes tend to be falsely classified as having present transcripts. Correction of non-specific binding for both perfect-match and mismatch probes using probe-sequence models can partially remove the probe-sequence bias and result in better performance of the MAS 5.0 algorithm.
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spelling pubmed-23947742008-05-24 Correcting for sequence biases in present/absent calls Schuster, Eugene F Blanc, Eric Partridge, Linda Thornton, Janet M Genome Biol Method The probe sequence of short oligonucleotides in Affymetrix microarray experiments can have a significant influence on present/absent calls of probesets with absent target transcripts. Probesets enriched for central Ts and depleted of central As in the perfect-match probes tend to be falsely classified as having present transcripts. Correction of non-specific binding for both perfect-match and mismatch probes using probe-sequence models can partially remove the probe-sequence bias and result in better performance of the MAS 5.0 algorithm. BioMed Central 2007 2007-06-26 /pmc/articles/PMC2394774/ /pubmed/17594492 http://dx.doi.org/10.1186/gb-2007-8-6-r125 Text en Copyright © 2007 Schuster et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an open access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Method
Schuster, Eugene F
Blanc, Eric
Partridge, Linda
Thornton, Janet M
Correcting for sequence biases in present/absent calls
title Correcting for sequence biases in present/absent calls
title_full Correcting for sequence biases in present/absent calls
title_fullStr Correcting for sequence biases in present/absent calls
title_full_unstemmed Correcting for sequence biases in present/absent calls
title_short Correcting for sequence biases in present/absent calls
title_sort correcting for sequence biases in present/absent calls
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2394774/
https://www.ncbi.nlm.nih.gov/pubmed/17594492
http://dx.doi.org/10.1186/gb-2007-8-6-r125
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